Matthew Hj Cordes

Interests

Teaching

biochemistry; structural biology

Research

protein evolution; protein structure; protein folding; protein toxins; NMR spectroscopy

Courses

Scholarly Contributions

Journals/Publications

• Andreatta, M. E., Levine, J. A., Foy, S. G., Guzman, L. D., Kosinski, L. J., Cordes, M. H., & Masel, J. (2015). The Recent De Novo Origin of Protein C-Termini. Genome biology and evolution, 7(6), 1686-701.
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  Protein-coding sequences can arise either from duplication and divergence of existing sequences, or de novo from noncoding DNA. Unfortunately, recently evolved de novo genes can be hard to distinguish from false positives, making their study difficult. Here, we study a more tractable version of the process of conversion of noncoding sequence into coding: the co-option of short segments of noncoding sequence into the C-termini of existing proteins via the loss of a stop codon. Because we study recent additions to potentially old genes, we are able to apply a variety of stringent quality filters to our annotations of what is a true protein-coding gene, discarding the putative proteins of unknown function that are typical of recent fully de novo genes. We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic. We find one putative gene fusion that turns out, on close inspection, to be the product of replicated assembly errors, further highlighting the issue of false positives in the study of rare events. Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure.
• Eaton, K. V., Anderson, W. J., Dubrava, M. S., Kumirov, V. K., Dykstra, E. M., & Cordes, M. H. (2015). Studying protein fold evolution with hybrids of differently folded homologs. Protein engineering, design & selection : PEDS, 28(8), 241-50.
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  To study the sequence determinants governing protein fold evolution, we generated hybrid sequences from two homologous proteins with 40% identity but different folds: Pfl 6 Cro, which has a mixed α + β structure, and Xfaso 1 Cro, which has an all α-helical structure. First, we first examined eight chimeric hybrids in which the more structurally conserved N-terminal half of one protein was fused to the more structurally divergent C-terminal half of the other. None of these chimeras folded, as judged by circular dichroism spectra and thermal melts, suggesting that both halves have strong intrinsic preferences for the native global fold pattern, and/or that the interfaces between the halves are not readily interchangeable. Second, we examined 10 hybrids in which blocks of the structurally divergent C-terminal region were exchanged. These hybrids showed varying levels of thermal stability and suggested that the key residues in the Xfaso 1 C terminus specifying the all-α fold were concentrated near the end of helix 4 in Xfaso 1, which aligns to the end of strand 2 in Pfl 6. Finally, we generated hybrid substitutions for each individual residue in this critical region and measured thermal stabilities. The results suggested that R47 and V48 were the strongest factors that excluded formation of the α + β fold in the C-terminal region of Xfaso 1. In support of this idea, we found that the folding stability of one of the original eight chimeras could be rescued by back-substituting these two residues. Overall, the results show not only that the key factors for Cro fold specificity and evolution are global and multifarious, but also that some all-α Cro proteins have a C-terminal subdomain sequence within a few substitutions of switching to the α + β fold.
• Lajoie, D. M., & Cordes, M. H. (2015). Spider, bacterial and fungal phospholipase D toxins make cyclic phosphate products. Toxicon : official journal of the International Society on Toxinology, 108, 176-80.
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  Phospholipase D (PLD) toxins from sicariid spiders, which cause disease in mammals, were recently found to convert their primary substrates, sphingomyelin and lysophosphatidylcholine, to cyclic phospholipids. Here we show that two PLD toxins from pathogenic actinobacteria and ascomycete fungi, which share distant homology with the spider toxins, also generate cyclic phospholipids. This shared function supports divergent evolution of the PLD toxins from a common ancestor and suggests the importance of cyclic phospholipids in pathogenicity.
• Lajoie, D. M., Roberts, S. A., Zobel-Thropp, P. A., Delahaye, J. L., Bandarian, V., Binford, G. J., & Cordes, M. H. (2015). Variable Substrate Preference Among Phospholipase D Toxins From Sicariid Spiders. Journal of Biological Chemistry.
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  Venoms of the sicariid spiders contain phospholipase D enzyme toxins that cause severe dermonecrosis and even death in humans. These enzymes convert sphingolipid and lysolipid substrates to cyclic phosphates by activating a hydroxyl nucleophile present in both classes of lipid. The most medically relevant substrates are thought to be sphingomyelin and/or lysophosphatidylcholine, which are common lipids in mammals. To better understand the substrate preference of these toxins, we used 31P-NMR to compare the activity of three related but phylogenetically diverse sicariid toxins against a diverse panel of sphingolipid and lysolipid substrates. Two of the three showed significantly faster turnover of sphingolipids over lysolipids, and all three showed a strong preference for positively charged (choline and/or ethanolamine) over neutral (glycerol and serine) head groups. Strikingly, however, the enzymes vary widely in their preference for choline, the head group of both sphingomyelin and lysophosphatidylcholine, versus ethanolamine. An enzyme from Sicarius terrosus showed a strong preference for ethanolamine over choline, while two paralogous enzymes from Loxosceles arizonica either preferred choline or showed no significant preference. Intrigued by the novel substrate preference of the Sicarius enzyme, we solved its crystal structure at 2.1 A resolution. The evolution of variable substrate specificity may help explain the reduced dermonecrotic potential of some natural toxin variants, because mammalian sphingolipids use primarily choline as a positively charged head group; it may also be relevant for sicariid predatory behavior, because ethanolamine-containing sphingolipids are common in insect prey.
• Lajoie, D. M., Zobel-Thropp, P. A., Kumirov, V. K., Bandarian, V., Binford, G. J., & Cordes, M. H. (2013). Phospholipase D toxins of brown spider venom convert lysophosphatidylcholine and sphingomyelin to cyclic phosphates. PLoS ONE, 8(8).
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  Venoms of brown spiders in the genus Loxosceles contain phospholipase D enzyme toxins that can cause severe dermonecrosis and even death in humans. These toxins cleave the substrates sphingomyelin and lysophosphatidylcholine in mammalian tissues, releasing the choline head group. The other products of substrate cleavage have previously been reported to be monoester phospholipids, which would result from substrate hydrolysis. Using (31)P NMR and mass spectrometry we demonstrate that recombinant toxins, as well as whole venoms from diverse Loxosceles species, exclusively catalyze transphosphatidylation rather than hydrolysis, forming cyclic phosphate products from both major substrates. Cyclic phosphates have vastly different biological properties from their monoester counterparts, and they may be relevant to the pathology of brown spider envenomation.
• Stewart, K. L., Dodds, E. D., Wysocki, V. H., & Cordes, M. H. (2013). A polymetamorphic protein. Protein Science, 22(5).
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  Arc repressor is a homodimeric protein with a ribbon-helix-helix fold. A single polar-to-hydrophobic substitution (N11L) at a solvent-exposed position leads to population of an alternate dimeric fold in which 3₁₀ helices replace a β-sheet. Here we find that the variant Q9V/N11L/R13V (S-VLV), with two additional polar-to-hydrophobic surface mutations in the same β-sheet, forms a highly stable, reversibly folded octamer with approximately half the α-helical content of wild-type Arc. At low protein concentration and low ionic strength, S-VLV also populates both dimeric topologies previously observed for N11L, as judged by NMR chemical shift comparisons. Thus, accumulation of simple hydrophobic mutations in Arc progressively reduces fold specificity, leading first to a sequence with two folds and then to a manifold bridge sequence with at least three different topologies. Residues 9-14 of S-VLV form a highly hydrophobic stretch that is predicted to be amyloidogenic, but we do not observe aggregates of higher order than octamer. Increases in sequence hydrophobicity can promote amyloid aggregation but also exert broader and more complex effects on fold specificity. Altered native folds, changes in fold coupled to oligomerization, toxic pre-amyloid oligomers, and amyloid fibrils may represent a near continuum of accessible alternatives in protein structure space.
• Stewart, K. L., Nelson, M. R., Eaton, K. V., Anderson, W. J., & Cordes, M. H. (2013). A role for indels in the evolution of Cro protein folds. Proteins, 81(11).
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  Insertions and deletions in protein sequences, or indels, can disrupt structure and may result in changes in protein folds during evolution or in association with alternative splicing. Pfl 6 and Xfaso 1 are two proteins in the Cro family that share a common ancestor but have different folds. Sequence alignments of the two proteins show two gaps, one at the N terminus, where the sequence of Xfaso 1 is two residues shorter, and one near the center of the sequence, where the sequence of Pfl 6 is five residues shorter. To test the potential importance of indels in Cro protein evolution, we generated hybrid variants of Pfl 6 and Xfaso 1 with indels in one or both regions, chosen according to several plausible sequence alignments. All but one deletion variant completely unfolded both proteins, showing that a longer N-terminal sequence was critical for Pfl 6 folding and a longer central region sequence was critical for Xfaso 1 folding. By contrast, Xfaso 1 tolerated a longer N-terminal sequence with little destabilization, and Pfl 6 tolerated central region insertions, albeit with substantial effects on thermal stability and some perturbation of the surrounding structure. None of the mutations appeared to convert one stable fold into the other. On the basis of this two-protein comparison, short insertion and deletion mutations probably played a role in evolutionary fold change in the Cro family, but were also not the only factors. Proteins 2013; 81:1988-1996. © 2013 Wiley Periodicals, Inc.
• Cordes, M. H., & Stewart, K. L. (2012). The porous borders of the protein world. Structure, 20(2), 199-200.
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  PMID: 22325767;Abstract: Fold switching may play a role in the evolution of new protein folds and functions. He et al., in this issue of Structure, use protein design to illustrate that the same drastic change in a protein fold can occur via multiple different mutational pathways. © 2012 Elsevier Ltd. All rights reserved.
• Anderson, W. J., Van Dorn, L. O., Ingram, W. M., & Cordes, M. H. (2011). Evolutionary bridges to new protein folds: design of C-terminal Cro protein chameleon sequences. Protein Engineering, Design & Selection : PEDS, 24(9).
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  Regions of amino-acid sequence that are compatible with multiple folds may facilitate evolutionary transitions in protein structure. In a previous study, we described a heuristically designed chameleon sequence (SASF1, structurally ambivalent sequence fragment 1) that could adopt either of two naturally occurring conformations (α-helical or β-sheet) when incorporated as part of the C-terminal dimerization subdomain of two structurally divergent transcription factors, P22 Cro and λ Cro. Here we describe longer chameleon designs (SASF2 and SASF3) that in the case of SASF3 correspond to the full C-terminal half of the ordered region of a P22 Cro/λ Cro sequence alignment (residues 34-57). P22-SASF2 and λ(WDD)-SASF2 show moderate thermal stability in denaturation curves monitored by circular dichroism (T(m) values of 46 and 55°C, respectively), while P22-SASF3 and λ(WDD)-SASF3 have somewhat reduced stability (T(m) values of 33 and 49°C, respectively). (13)C and (1)H NMR secondary chemical shift analysis confirms two C-terminal α-helices for P22-SASF2 (residues 36-45 and 54-57) and two C-terminal β-strands for λ(WDD)-SASF2 (residues 40-45 and 50-52), corresponding to secondary structure locations in the two parent sequences. Backbone relaxation data show that both chameleon sequences have a relatively well-ordered structure. Comparisons of (15)N-(1)H correlation spectra for SASF2 and SASF3-containing proteins strongly suggest that SASF3 retains the chameleonism of SASF2. Both Cro C-terminal conformations can be encoded in a single sequence, showing the plausibility of linking different Cro folds by smooth evolutionary transitions. The N-terminal subdomain, though largely conserved in structure, also exerts an important contextual influence on the structure of the C-terminal region.
• Bouvignies, G., Vallurupalli, P., Cordes, M. H., Hansen, D., & Kay, L. E. (2011). Measuring ¹H^N temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy. Journal of Biomolecular NMR, 50(1), 13-18.
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  PMID: 21424227;PMCID: PMC3229278;Abstract: A method based on the Carr-Purcell-Meiboom- Gill relaxation dispersion experiment is presented for measuring the temperature coefficients of amide proton chemical shifts of low populated 'invisible' protein states that exchange with a 'visible' ground state on the millisecond time-scale. The utility of the approach is demonstrated with an application to an I58D mutant of the Pfl6 Cro protein that undergoes exchange between the native, folded state and a cold denatured, unfolded conformational ensemble that is populated at a level of 6% at 2.5°C. A wide distribution of amide temperature coefficients is measured for the unfolded state. The distribution is centered about -5.6 ppb/K, consistent with an absence of intra-molecular hydrogen bonds, on average. However, the large range of values (standard deviation of 2.1 ppb/K) strongly supports the notion that the unfolded state of the protein is not a true random coil polypeptide chain. © Springer Science+Business Media B.V. 2011.
• Dodds, E. D., Blackwell, A. E., Jones, C. M., Holso, K. L., O'Brien, D. J., Cordes, M. H., & Wysocki, V. H. (2011). Determinants of gas-phase disassembly behavior in homodimeric protein complexes with related yet divergent structures. Analytical Chemistry, 83(10), 3881-3889.
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  PMID: 21486017;PMCID: PMC3094495;Abstract: The overall structure of a protein-protein complex reflects an intricate arrangement of noncovalent interactions. Whereas intramolecular interactions confer secondary and tertiary structure to individual subunits, intermolecular interactions lead to quaternary structure-the ordered aggregation of separate polypeptide chains into multisubunit assemblies. The specific ensemble of noncovalent contacts dictates the stability of subunit folds, enforces protein-protein binding specificity, and determines multimer stability. Consequently, noncovalent architecture is likely to play a role in the gas-phase dissociation of these assemblies during tandem mass spectrometry (MS/MS). To further advance the applicability of MS/MS to analytical problems in structural biology, a better understanding of the interplay between the structures and fragmentation behaviors of noncovalent protein complexes is essential. The present work constitutes a systematic study of model protein homodimers (bacteriophage N15 Cro, bacteriophage λ Cro, and bacteriophage P22 Arc) with related but divergent structures, both in terms of subunit folds and protein-protein interfaces. Because each of these dimers has a well-characterized structure (solution and/or crystal structure), specific noncovalent features could be correlated with gas-phase disassembly patterns as studied by collision-induced dissociation, surface-induced dissociation, and ion mobility. Of the several respects in which the dimers differed in structure, the presence or absence of intermolecular electrostatic contacts exerted the most significant influence on the gas-phase dissociation behavior. This is attributed to the well-known enhancement of ionic interactions in the absence of bulk solvent. Because salt bridges are general contributors to both intermolecular and intramolecular stability in protein complexes, these observations are broadly applicable to aid in the interpretation or prediction of dissociation spectra for noncovalent protein assemblies. © 2011 American Chemical Society.
• Hall, B. M., Vaughn, E. E., Begaye, A. R., & Cordes, M. H. (2011). Reengineering Cro protein functional specificity with an evolutionary code. Journal of Molecular Biology, 413(5).
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  Cro proteins from different lambdoid bacteriophages are extremely variable in their target consensus DNA sequences and constitute an excellent model for evolution of transcription factor specificity. We experimentally tested a bioinformatically derived evolutionary code relating switches between pairs of amino acids at three recognition helix sites in Cro proteins to switches between pairs of nucleotide bases in the cognate consensus DNA half-sites. We generated all eight possible code variants of bacteriophage λ Cro and used electrophoretic mobility shift assays to compare binding of each variant to its own putative cognate site and to the wild-type cognate site; we also tested the wild-type protein against all eight DNA sites. Each code variant showed stronger binding to its putative cognate site than to the wild-type site, except some variants containing proline at position 27; each also bound its cognate site better than wild-type Cro bound the same site. Most code variants, however, displayed poorer affinity and specificity than wild-type λ Cro. Fluorescence anisotropy assays on λ Cro and the triple code variant (PSQ) against the two cognate sites confirmed the switch in specificity and showed larger apparent effects on binding affinity and specificity. Bacterial one-hybrid assays of λ Cro and PSQ against libraries of sequences with a single randomized half-site showed the expected switches in specificity at two of three coded positions and no clear switches in specificity at noncoded positions. With a few caveats, these results confirm that the proposed Cro evolutionary code can be used to reengineer Cro specificity.
• Bouvignies, G., Korzhnev, D. M., Neudecker, P., Hansen, D. F., H., M., & Kay, L. E. (2010). A simple method for measuring signs of 1HN chemical shift differences between ground and excited protein states. Journal of Biomolecular NMR, 47(2), 135-141.
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  PMID: 20428928;PMCID: PMC3034452;Abstract: NMR relaxation dispersion spectroscopy is a powerful method for studying protein conformational dynamics whereby visible, ground and invisible, excited conformers interconvert on the millisecond time-scale. In addition to providing kinetics and thermodynamics parameters of the exchange process, the CPMG dispersion experiment also allows extraction of the absolute values of the chemical shift differences between interconverting states, |δω̄|, opening the way for structure determination of excited state conformers. Central to the goal of structural analysis is the availability of the chemical shifts of the excited state that can only be obtained once the signs of δω̄ are known. Herein we describe a very simple method for determining the signs of 1HN δω̄ values based on a comparison of peak positions in the directly detected dimensions of a pair of 1HN-15N correlation maps recorded at different static magnetic fields. The utility of the approach is demonstrated for three proteins that undergo millisecond time-scale conformational rearrangements. Although the method provides fewer signs than previously published techniques it does have a number of strengths: (1) Data sets needed for analysis are typically available from other experiments, such as those required for measuring signs of 15N δω̄ values, thus requiring no additional experimental time, (2) acquisition times in the critical detection dimension can be as long as necessary and (3) the signs obtained can be used to cross-validate those from other approaches. © Springer Science+Business Media B.V. 2010.
• Binford, G. J., Bodner, M. R., Cordes, M. H., Baldwin, K. L., Rynerson, M. R., Burns, S. N., & Zobel-Thropp, P. A. (2009). Molecular evolution, functional variation, and proposed nomenclature of the gene family that includes sphingomyelinase D in sicariid spider venoms. Molecular Biology and Evolution, 26(3), 547-566.
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  PMID: 19042943;PMCID: PMC2767091;Abstract: The venom enzyme sphingomyelinase D (SMase D) in the spider family Sicariidae (brown or fiddleback spiders [Loxosceles] and six-eyed sand spiders [Sicarius]) causes dermonecrosis in mammals. SMase D is in a gene family with multiple venom-expressed members that vary in functional specificity. We analyze molecular evolution of this family and variation in SMase D activity among crude venoms using a data set that represents the phylogenetic breadth of Loxosceles and Sicarius. We isolated a total of 190 nonredundant nucleotide sequences encoding 168 nonredundant amino acid sequences of SMase D homologs from 21 species. Bayesian phylogenies support two major clades that we name α and β, within which we define seven and three subclades, respectively. Sequences in the α clade are exclusively from New World Loxosceles and Loxosceles rufescens and include published genes for which expression products have SMase D and dermonecrotic activity. The β clade includes paralogs from New World Loxosceles that have no, or reduced, SMase D and no dermonecrotic activity and also paralogs from Sicarius and African Loxosceles of unknown activity. Gene duplications are frequent, consistent with a birth-and-death model, and there is evidence of purifying selection with episodic positive directional selection. Despite having venom-expressed SMase D homologs, venoms from New World Sicarius have reduced, or no, detectable SMase D activity, and Loxosceles in the Southern African spinulosa group have low SMase D activity. Sequence conservation mapping shows >98% conservation of proposed catalytic residues of the active site and around a plug motif at the opposite end of the TIM barrel, but α and β clades differ in conservation of key residues surrounding the apparent substrate binding pocket. Based on these combined results, we propose an inclusive nomenclature for the gene family, renaming it SicTox, and discuss emerging patterns of functional diversification. © The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.
• Dubrava, M. S., Ingram, W. M., Roberts, S. A., Weichsel, A., Montfort, W. R., & Cordes, M. H. (2008). N15 Cro and lambda Cro: orthologous DNA-binding domains with completely different but equally effective homodimer interfaces. Protein Science, 17(5).
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  Bacteriophage Cro proteins bind to target DNA as dimers but do not all dimerize with equal strength, and differ in fold in the region of the dimer interface. We report the structure of the Cro protein from Enterobacteria phage N15 at 1.05 A resolution. The subunit fold contains five alpha-helices and is closely similar to the structure of P22 Cro (1.3 A backbone room mean square difference over 52 residues), but quite different from that of lambda Cro, a structurally diverged member of this family with a mixed alpha-helix/beta-sheet fold. N15 Cro crystallizes as a biological dimer with an extensive interface (1303 A(2) change in accessible surface area per dimer) and also dimerizes in solution with a K(d) of 5.1 +/- 1.5 microM. Its dimerization is much stronger than that of its structural homolog P22 Cro, which does not self-associate detectably in solution. Instead, the level of self-association and interfacial area for N15 Cro is similar to that of lambda Cro, even though these two orthologs do not share the same fold and have dimer interfaces that are qualitatively different in structure. The common Cro ancestor is thought to be an all-helical monomer similar to P22 Cro. We propose that two Cro descendants independently developed stronger dimerization by entirely different mechanisms.
• Hall, B. M., Roberts, S. A., Heroux, A. M., & Cordes, M. H. (2008). Two structures of a lambda Cro variant highlight dimer flexibility but disfavor major dimer distortions upon specific binding of cognate DNA. Journal of Molecular Biology, 375(3).
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  Previously reported crystal structures of free and DNA-bound dimers of lambda Cro differ strongly (about 4 A backbone rmsd), suggesting both flexibility of the dimer interface and induced-fit protein structure changes caused by sequence-specific DNA binding. Here, we present two crystal structures, in space groups P3(2)21 and C2 at 1.35 and 1.40 A resolution, respectively, of a variant of lambda Cro with three mutations in its recognition helix (Q27P/A29S/K32Q, or PSQ for short). One dimer structure (P3(2)21; PSQ form 1) resembles the DNA-bound wild-type Cro dimer (1.0 A backbone rmsd), while the other (C2; PSQ form 2) resembles neither unbound (3.6 A) nor bound (2.4 A) wild-type Cro. Both PSQ form 2 and unbound wild-type dimer crystals have a similar interdimer beta-sheet interaction between the beta1 strands at the edges of the dimer. In the former, an infinite, open beta-structure along one crystal axis results, while in the latter, a closed tetrameric barrel is formed. Neither the DNA-bound wild-type structure nor PSQ form 1 contains these interdimer interactions. We propose that beta-sheet superstructures resulting from crystal contact interactions distort Cro dimers from their preferred solution conformation, which actually resembles the DNA-bound structure. These results highlight the remarkable flexibility of lambda Cro but also suggest that sequence-specific DNA binding may not induce large changes in the protein structure.
• Narra, H. P., Cordes, M. H., & Ochman, H. (2008). Structural features and the persistence of acquired proteins. Proteomics, 8(22), 4772-4781.
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  PMID: 18924109;PMCID: PMC3014317;Abstract: ORFan genes can constitute a large fraction of a bacterial genome, but due to their lack of homologs, their functions have remained largely unexplored. To determine if particular features of ORFan-encoded proteins promote their presence in a genome, we analyzed properties of ORFans that originated over a broad evolutionary timescale. We also compared ORFan genes to another class of acquired genes, heterogeneous occurrence in prokaryotes (HOPs), which have homologs in other bacteria. A total of 54 ORFan and HOP genes selected from different phylogenetic depths in the Escherichia coli lineage were cloned, expressed, purified, and subjected to circular dichroism (CD) spectroscopy. A majority of genes could be expressed, but only 18 yielded sufficient soluble protein for spectral analysis. Of these, half were significantly α-helical, three were predominantly b-sheet, and six were of intermediate/indeterminate structure. Although a higher proportion of HOPs yielded soluble proteins with resolvable secondary structures, ORFans resembled HOPs with regard to most of the other features tested. Overall, we found that those ORFan and HOP genes that have persisted in the E. coli lineage were more likely to encode soluble and folded proteins, more likely to display environmental modulation of their gene expression, and by extrapolation, are more likely to be functional. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA.
• Roessler, C. G., Hall, B. M., Anderson, W. J., Ingram, W. M., Roberts, S. A., Montfort, W. R., & Cordes, M. H. (2008). Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds. Proceedings of the National Academy of Sciences of the United States of America, 105(7).
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  Proteins that share common ancestry may differ in structure and function because of divergent evolution of their amino acid sequences. For a typical diverse protein superfamily, the properties of a few scattered members are known from experiment. A satisfying picture of functional and structural evolution in relation to sequence changes, however, may require characterization of a larger, well chosen subset. Here, we employ a "stepping-stone" method, based on transitive homology, to target sequences intermediate between two related proteins with known divergent properties. We apply the approach to the question of how new protein folds can evolve from preexisting folds and, in particular, to an evolutionary change in secondary structure and oligomeric state in the Cro family of bacteriophage transcription factors, initially identified by sequence-structure comparison of distant homologs from phages P22 and lambda. We report crystal structures of two Cro proteins, Xfaso 1 and Pfl 6, with sequences intermediate between those of P22 and lambda. The domains show 40% sequence identity but differ by switching of alpha-helix to beta-sheet in a C-terminal region spanning approximately 25 residues. Sedimentation analysis also suggests a correlation between helix-to-sheet conversion and strengthened dimerization.
• Degnan, P. H., Michalowski, C. B., Babić, A. C., Cordes, M. H., & Little, J. W. (2007). Conservation and diversity in the immunity regions of wild phages with the immunity specificity of phage λ. Molecular Microbiology, 64(1), 232-244.
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  PMID: 17376085;Abstract: The gene regulatory circuitry of phage λ is among the best-understood circuits. Much of the circuitry centres around the immunity region, which includes genes for two repressors, CI and Cro, and their cis-acting sites. Related phages, termed lambdoid phages, have different immunity regions, but similar regulatory circuitry and genome organization to that of λ, and show a mosaic organization, arising by recombination between lambdoid phages. We sequenced the immunity regions of several wild phages with the immunity specificity of λ, both to determine whether natural variation exists in regulation, and to analyse conservation and variability in a region rich in well-studied regulatory elements. CI, Cro and their cis-acting sites are almost identical to those in λ, implying that regulatory mechanisms controlled by the immunity region are conserved. A segment adjacent to one of the operator regions is also conserved, and may be a novel regulatory element. In most isolates, different alleles of two regulatory proteins (N and CII) flank the immunity region; possibly the lysis-lysogeny decision is more variable among isolates. Extensive mosaicism was observed for several elements flanking the immunity region. Very short sequence elements or microhomologies were also identified. Our findings suggest mechanisms by which fine-scale mosaicism arises. © 2007 The Authors.
• Cordes, M. H., & Binford, G. J. (2006). Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria. Bioinformatics, 22(3), 264-268.
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  PMID: 16332712;Abstract: Motivation: Spiders in the genus Loxosceles, including the notoriously toxic brown recluse, cause severe necrotic skin lesions owing to the presence of a venom enzyme called sphingomyelinase D (SMaseD). This enzyme activity is unknown elsewhere in the animal kingdom but is shared with strains of pathogenic Corynebacteria that cause various illnesses in farm animals. The presence of the same toxic activity only in distantly related organisms poses an interesting and medically important question in molecular evolution. Results: We use superpositions of rece ntly determined structures and sequence comparisons to infer that both bacterial and spider SMaseDs originated from a common, broadly conserved domain family, the glycerophosphoryl diester phosphodiesterases. We also identify a unique sequence/structure motif present in both SMaseDs but not in the ancestral family, supporting SMaseD origin through a single divergence event in either bacteria or spiders, followed by lateral gene transfer from one lineage to the other. © The Author 2005. Published by Oxford University Press. All rights reserved.
• Newlove, T., Atkinson, K. R., Van Dorn, L. O., & Cordes, M. H. (2006). A trade between similar but nonequivalent intrasubunit and intersubunit contacts in Cro dimer evolution. Biochemistry, 45(20).
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  The homodimeric lambda Cro protein has a "ball-and-socket" interface that includes insertion of an aromatic side chain, Phe 58, from each subunit into a cavity in the hydrophobic core of the other subunit. This overlap between the subunit core and dimer interface hypothetically explains the strong dimerization and weak monomer stability of lambda Cro in comparison to homologues. According to a model developed here and in a previous study [LeFevre, K. R., and Cordes, M. H. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 2345-2350], the socket cavity evolved in part by replacement of a buried tryptophan in an ancestral stable monomer with a smaller side chain (Ala 33 in lambda Cro). The resulting core defect was in effect repaired by insertion of a different side chain (Phe 58) from a second subunit, generating the ball and socket. Consistent with such an evolutionary trade between intrasubunit and intersubunit interactions, we showed in the previous study that restoration of the ancestral Trp 33 in lambda Cro stabilized the monomer and reduced the extent of dimerization. Here, we report the solution structure of a stable lambda Cro monomer containing the Ala33Trp mutation, which confirms that the restored tryptophan fulfills its ancestral role as a core side chain, filling part of the socket cavity occupied by Phe 58 in the wild-type dimer. The structure also reveals, however, that the cavity is not completely filled by Trp 33, suggesting that its formation could have involved multiple mutations that reduced side chain volume. We offer suggestive evidence of a role of mutations at a second position.
• Patki, A. U., Hausrath, A. C., & Cordes, M. H. (2006). High polar content of long buried blocks of sequence in protein domains suggests selection against amyloidogenic non-polar sequences. Journal of Molecular Biology, 362(4).
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  Native protein structures achieve stability in part by burying hydrophobic side-chains. About 75% of all amino acid residues buried in protein interiors are non-polar. Buried residues are not uniformly distributed in protein sequences, but sometimes cluster as contiguous polypeptide stretches that run through the interior of protein domain structures. Such regions have an intrinsically high local sequence density of non-polar residues, creating a potential problem: local non-polar sequences also promote protein misfolding and aggregation into non-native structures such as the amyloid fibrils in Alzheimer's disease. Here we show that long buried blocks of sequence in protein domains of known structure have, on average, a lower content of non-polar amino acids (about 70%) than do isolated buried residues (about 80%). This trend is observed both in small and in large protein domains and is independent of secondary structure. Long, completely non-polar buried stretches containing many large side-chains are particularly avoided. Aspartate residues that are incorporated in long buried stretches were found to make fewer polar interactions than those in short stretches, hinting that they may be destabilizing to the native state. We suggest that evolutionary pressure is acting on non-native properties, causing buried polar residues to be placed at positions where they would break up aggregation-prone non-polar sequences, perhaps even at some cost to native state stability.
• Van Dorn, L. O., Newlove, T., Chang, S., Ingram, W. M., & Cordes, M. H. (2006). Relationship between sequence determinants of stability for two natural homologous proteins with different folds. Biochemistry, 45(35).
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  In the Cro protein family, an evolutionary change in secondary structure has converted an alpha-helical fold to a mixture of alpha-helix and beta-sheet. P22 Cro and lambda Cro represent the ancestral all-alpha and descendant alpha+beta folds, respectively. The major structural differences between these proteins are at the C-terminal end of the domain (residues 34-56), where two alpha-helices in P22 Cro align with two beta-strands in lambda Cro. We sought to assess the possibility that smooth evolutionary transitions could have converted the all-alpha structure to the alpha+beta structure through sequences that could adopt both folds. First, we used scanning mutagenesis to identify and compare patterns of key stabilizing residues in the C-terminal regions of both P22 Cro and lambda Cro. These patterns exhibited little similarity to each other, with structurally important residues in the two proteins most often occurring at different sequence positions. Second, "hybrid scanning" studies, involving replacement of each wild-type residue in P22 Cro with the aligned wild-type residue in lambda Cro and vice versa, revealed five or six residues in each protein that strongly destabilized the other. These results suggest that key stability determinants for each Cro fold are quite different and that the P22 Cro sequence strongly favors the all-alpha structure while the lambda Cro sequence strongly favors the alpha+beta structure. Nonetheless, we were able to design a "structurally ambivalent" sequence fragment (SASF1), which corresponded to residues 39-56 and simultaneously incorporated most key stabilizing residues for both P22 Cro and lambda Cro. NMR experiments showed SASF1 to stably fold as a beta-hairpin when incorporated into the lambda Cro sequence but as a pair of alpha-helices when incorporated into P22 Cro.
• Anderson, T. A., Cordes, M. H., & Sauer, R. T. (2005). Sequence determinants of a conformational switch in a protein structure. Proceedings of the National Academy of Sciences of the United States of America, 102(51), 18344-18349.
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  PMID: 16344489;PMCID: PMC1317976;Abstract: The Arc repressor of bacteriophage P22 is a dimeric member of the ribbon-helix-helix family of transcription factors. Residues 9-14 of each wild-type Arc subunit pair to form two antiparallel -strands and have the alternating pattern of polar and nonpolar residues expected for a β-ribbon with one solvent-exposed face and one face that forms part of the hydrophobic core. Simultaneously switching Asn-11 to Leu and Leu-12 to Asn changes the local binary sequence pattern to that of an amphipathic helix. Previous studies have shown that this double mutation results in replacement of the wild-type β-ribbon by two right-handed Biohelices. Moreover, an Arc variant bearing just the Asn-11 → Leu mutation has an ambiguous binary pattern and can form either the ribbon or the helical structures, which interchange rapidly. Here, we study Arc mutants in which position 11 is occupied by Gly, Ala, Val, Ile, Leu, Met, Phe, or Tyr. These mutants adopt the wild-type β-ribbon structure in a sequence context that stabilizes this fold, but they assume the alternative helical structure in a sequence background in which the wild-type fold is precluded by negative design. In an otherwise wild-type sequence background, the detailed chemical properties of the position 11 side chain dictate which of the two competing conformational folds is preferred. © 2005 by The National Academy of Sciences of the USA.
• Binford, G. J., Cordes, M. H., & Wells, M. A. (2005). Sphingomyelinase D from venoms of Loxosceles spiders: Evolutionary insights from cDNA sequences and gene structure. Toxicon, 45(5), 547-560.
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  PMID: 15777950;Abstract: Loxosceles spider venoms cause dermonecrosis in mammalian tissues. The toxin sphingomyelinase D (SMaseD) is a sufficient causative agent in lesion formation and is only known in these spiders and a few pathogenic bacteria. Similarities between spider and bacterial SMaseD in molecular weights, pIs and N-terminal amino acid sequence suggest an evolutionary relationship between these molecules. We report three cDNA sequences from venom-expressed mRNAs, analyses of amino acid sequences, and partial characterization of gene structure of SMaseD homologs from Loxosceles arizonica with the goal of better understanding the evolution of this toxin. Sequence analyses indicate SMaseD is a single domain protein and a divergent member of the ubitiquous, broadly conserved glycerophosphoryl diester phosphodiesterase family (GDPD). Bacterial SMaseDs are not identifiable as homologs of spider SMaseD or GDPD family members. Amino acid sequence similarities do not afford clear distinction between independent origin of toxic SMaseD activity in spiders and bacteria and origin in one lineage by ancient horizontal transfer from the other. The SMaseD genes span at least 6500 bp and contain at least 5 introns. Together, these data indicate L. arizonica SMaseD has been evolving within a eukaryotic genome for a long time ruling out origin by recent transfer from bacteria. © 2004 Elsevier Ltd. All rights reserved.
• Hall, B. M., Lefevre, K. R., & Cordes, M. H. (2005). Sequence correlations between Cro recognition helices and cognate O(R) consensus half-sites suggest conserved rules of protein-DNA recognition. Journal of Molecular Biology, 350(4).
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  The O(R) regions from several lambdoid bacteriophages contain the three regulatory sites O(R)1, O(R)2 and O(R)3, to which the Cro and CI proteins can bind. These sites show imperfect dyad symmetry, have similar sequences, and generally lie on the same face of the DNA double helix. We have developed a computational method, which analyzes the O(R) regions of additional phages and predicts the location of these three sites. After tuning the method to predict known O(R) sites accurately, we used it to predict unknown sites, and ultimately compiled a database of 32 known and predicted O(R) binding site sets. We then identified sequences of the recognition helices (RH) for the cognate Cro proteins through manual inspection of multiple sequence alignments. Comparison of Cro RH and consensus O(R) half-site sequences revealed strong one-to-one correlations between two amino acids at each of three RH positions and two bases at each of three half-site positions (H1-->2, H3-->5 and H6-->6). In each of these three cases, one of the two amino acid/base-pairings corresponds to a contact observed in the crystal structure of a lambda Cro/consensus operator complex. The alternate amino acid/base combinations were rationalized using structural models. We suggest that the pairs of amino acid residues act as binary switches that efficiently modulate specificity for different consensus half-site variants during evolution. The observation of structurally reasonable amino acid-to-base correlations suggests that Cro proteins share some common rules of recognition despite their functional and structural diversity.
• McKnight, C. J., & Cordes, M. H. (2005). Networking at the Protein Society symposium.. Nature Chemical Biology, 1(5), 239-242.
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  PMID: 16408046;Abstract: From the complex behavior of multicomponent signaling networks to the structures of large protein complexes and aggregates, questions once viewed as daunting are now being tackled fearlessly by protein scientists. The 19th Annual Symposium of the Protein Society in Boston highlighted the maturation of systems biology as applied to proteins.
• Newlove, T., Konieczka, J. H., & Cordes, M. H. (2004). Secondary structure switching in Cro protein evolution. Structure, 12(4).
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  We report the solution structure of the Cro protein from bacteriophage P22. Comparisons of its sequence and structure to those of lambda Cro strongly suggest an alpha-to-beta secondary structure switching event during Cro evolution. The folds of P22 Cro and lambda Cro share a three alpha helix fragment comprising the N-terminal half of the domain. However, P22 Cro's C terminus folds as two helices, while lambda Cro's folds as a beta hairpin. The all-alpha fold found for P22 Cro appears to be ancestral, since it also occurs in cI proteins, which are anciently duplicated paralogues of Cro. PSI-BLAST and transitive homology analyses strongly suggest that the sequences of P22 Cro and lambda Cro are globally homologous despite encoding different folds. The alpha+beta fold of lambda Cro therefore likely evolved from its all-alpha ancestor by homologous secondary structure switching, rather than by nonhomologous replacement of both sequence and structure.
• Cordes, M. H., Walsh, N. P., McKnight, C. J., & Sauer, R. T. (2003). Solution structure of switch Arc, a mutant with 3₁₀ helices replacing a wild-type β-ribbon. Journal of Molecular Biology, 326(3), 899-909.
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  PMID: 12581649;Abstract: Adjacent N11L and L12N mutations in the antiparallel β-ribbon of Arc repressor result in dramatic changes in local structure in which each β-strand is replaced by a right-handed helix. The full solution structure of this "switch" Arc mutant shows that irregular 310 helices compose the new secondary structure. This structural metamorphosis conserves the number of main-chain and side-chain to main-chain hydrogen bonds and the number of fully buried core residues. Apart from a slight widening of the interhelical angle between α-helices A and B and changes in side-chain conformation of a few core residues in Arc, no large-scale structural adjustments in the remainder of the protein are necessary to accommodate the ribbon-to-helix change. Nevertheless, some changes in hydrogen-exchange rates are observed, even in regions that have very similar structures in the two proteins. The surface of switch Arc is packed poorly compared to wild-type, leading to ∼1000Å2 of additional solvent-accessible surface area, and the N termini of the 310 helices make unfavorable head-to-head electrostatic interactions. These structural features account for the positive m value and salt dependence of the ribbon-to-helix transition in Arc-N11L, a variant that can adopt either the mutant or wild-type structures. The tertiary fold is capped in different ways in switch and wild-type Arc, showing how stepwise evolutionary transformations can arise through small changes in amino acid sequence. © 2003 Elsevier Science Ltd. All rights reserved.
• LeFevre, K. R., & Cordes, M. H. (2003). Retroevolution of lambda Cro toward a stable monomer. Proceedings of the National Academy of Sciences of the United States of America, 100(5).
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  The Cro protein from bacteriophage lambda has a dimeric alpha+beta fold that evolved from an ancestral all-alpha monomer. The sequence mutations responsible for this dramatic structural evolution are unknown. Here we use analysis of sequence alignments to show that Ala-33, a small side chain in the hydrophobic "ball-and-socket" dimer interface of lambda Cro, was a much larger tryptophan side chain at a previous point in evolution. The retroevolutionary lambda Cro-A33W mutant shows a 10-fold reduction in dimerization affinity relative to the wild type as well as a large increase in monomer thermal stability (Delta T(m) > 10 degrees C), apparently due to partial filling of the hydrophobic socket from within the same monomer. An additional mutation in the dimer interface, F58D, almost completely abolishes detectable dimerization while maintaining the high monomer stability. The secondary structure content of the monomerized versions of lambda Cro is similar to that of the wild-type protein, and the tertiary structure of the monomer appears relatively well defined. These results (i) support a model in which the ball-and-socket dimer interface of lambda Cro was created by altered volume mutations within a limited branch of the Cro lineage and (ii) suggest the possibility that the evolution of the alpha+beta dimer from an all-alpha monomer proceeded through an alpha+beta monomer intermediate.
• Cordes, M. H., Burton, R. E., Walsh, N. P., McKnight, C. J., & Sauer, R. T. (2000). An evolutionary bridge to a new protein fold. Nature Structural Biology, 7(12), 1129-1132.
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  PMID: 11101895;Abstract: Arc repressor bearing the N11L substitution (Arc-N11L) is an evolutionary intermediate between the wild type protein, in which the region surrounding position 11 forms a β-sheet, and a double mutant 'switch Arc', in which this region is helical. Here, Arc-N11L is shown to be able to adopt either the wild type or mutant conformations. Exchange between these structures occurs on the millisecond time scale in a dynamic equilibrium in which the relative populations of each fold depend on temperature, solvent conditions and ligand binding. The N11L mutation serves as an evolutionary bridge from the β-sheet to the helical fold because in the mutant, Leu is an integral part of the hydrophobic core of the new structure but can also occupy a surface position in the wild type structure. Conversely, the polar Asn 11 side chain serves as a negative design element in wild type Arc because it cannot be incorporated into the core of the mutant fold.
• Cordes, M. H., & Sauer, R. T. (1999). Tolerance of a protein to multiple polar-to-hydrophobic surface substitutions. Protein Science, 8(2), 318-325.
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  PMID: 10048325;PMCID: PMC2144263;Abstract: Hydrophobic substitutions at solvent-exposed positions in two α- helical regions of the bacteriophage P22 Arc repressor were introduced by combinatorial mutagenesis. In helix A, hydrophobic residues were tolerated individually at each of the five positions examined, but multiple substitutions were poorly tolerated as shown by the finding that mutants with more than two additional hydrophobic residues were biologically inactive. Several inactive helix A variants were purified and found to have reduced thermal stability relative to wild-type Arc, with a rough correlation between the number of polar-to-hydrophobic substitutions and the magnitude of the stability defect. Quite different results were obtained in helix B, where variants with as many as five polar-to-hydrophobic substitutions were found to be biologically active and one variant with three hydrophobic substitutions had a t(m) 6 °C higher than wild-type. By contrast, a helix A mutant with three similar polar-to-hydrophobic substitutions was 23 °C less stable than wild-type. Also, one set of three polar-to-hydrophobic substitutions in helix B was tolerated when introduced into the wild-type background but not when introduced into an equally active mutant having a nearly identical structure. Context effects occur both when comparing different regions of the same protein and when comparing the same region in two different homologues.
• Cordes, M. H., Walsh, N. P., McKnight, C. J., & Sauer, R. T. (1999). Evolution of a protein fold in vitro. Science, 284(5412), 325-8.
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  A "switch" mutant of the Arc repressor homodimer was constructed by interchanging the sequence positions of a hydrophobic core residue, leucine 12, and an adjacent surface polar residue, asparagine 11, in each strand of an intersubunit beta sheet. The mutant protein adopts a fold in which each beta strand is replaced by a right-handed helix and side chains in this region undergo significant repacking. The observed structural changes allow the protein to maintain solvent exposure of polar side chains and optimal burial of hydrophobic side chains. These results suggest that new protein folds can evolve from existing folds without drastic or large-scale mutagenesis.
• Cordes, M. H., Davidson, A. R., & Sauer, R. T. (1996). Sequence space, folding and protein design. Current Opinion in Structural Biology, 6(1), 3-10.
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  PMID: 8696970;Abstract: Protein design efforts are beginning to yield molecules with many of the properties of natural proteins. Such experiments are informed by and contribute to our understanding of the sequence determinants of protein folding and stability. The most important design elements seem to be the proper placement of hydrophobic residues along the polypeptide chain and the ability of these residues to form a well packed core. Buried polar interactions, turn and capping motifs and secondary structural propensities also contribute, although probably to a lesser extent.
• H., M., & Berson, J. A. (1996). Medium effects on the rates of stereomutation of a pair of diastereomeric cyclopropanones. Ground state stabilization in nucleophilic solvents induces deviation from solvent polarity controlled behavior. Journal of the American Chemical Society, 118(26), 6241-6251.
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  Abstract: The synthesis of the two stereoisomers of spiro(bicyclo[2.2.1]heptane-2,1'-cyclopropan)-2'-one, 3a and 4a, from diazomethane and the ketene 2-carbonylylbicyclo[2.2.1]heptane in ether at 195 K yields a ~1.6 to 1 ratio. At 245 K, the ratio changes in a first-order manner, with an observed rate constant of 1.7 x 10-4 s-1, to an equilibrium ratio of 0.8 to 1. The temperature dependence of the interconversion of 3a and 4a (GC method) and that of their dideuterio derivatives 3b and 4b (NMR method) have been determined and yield activation parameters E(a) = 16.3 ± 1.4 kcal/mol and log A = 10.4 ± 1.4 (A in s-1) (GC method) and E(a) = 15.3 ± 1.4 and log A = 9.6 ± 1.4 (NMR method). The free energies of activation at 239 K have been determined in four solvents: dichloromethane (16.1 kcal/mol), acetone (17.7), hexane (17.9), and ether (19.1). The solvent dependence does not correlate well with commonly used measures of solvent polarity, and the reaction is unexpectedly slow in acetone and ether. This deceleration is explained in terms of nucleophilic association of these solvents with the carbonyl groups in the cyclopropanones, leading to a ground state stabilization.
• H., M., Gala, S. D., & Berson, J. A. (1994). Stereochemistry of a cyclopropanone by crystal structure analysis. The exo configuration of the diels-alder adduct of cyclopropenone and 1,3-diphenylisobenzofuran appears to be stabilized relative to the endo by an attractive ether-carbonyl interaction. Journal of the American Chemical Society, 116(24), 11161-11162.
• Bull, H. G., Thornberry, N. A., Cordes, M. H., & Patchett, A. A. (1985). Inhibition of rabbit lung angiotensin-converting enzyme by N(α)-[(S)-1-carboxy-3-phenylpropyl]L-alanyl-L-proline and N(α)-[(S)-1-carboxy-3-phenylpropyl]L-lysyl-L-proline. Journal of Biological Chemistry, 260(5), 2952-2962.
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  PMID: 2982845;Abstract: Two novel peptide analogs, N(α)-[(S)-1-carboxy-3-phenylpropyl]L-alanyl-L-proline and the corresponding L-lysyl-L-proline derivative, have been demonstrated to be potent competitive inhibitors of purified rabbit lung angiotensin-converting enzyme: K(i) = 2 and 1 x 10-10 M, respectively, at pH 7.5, 25°C, and 0.3 M chloride ion. Second-order rate constants for addition of these inhibitors to enzyme under the same conditions are in the range 1-2 x 106 M-1 s-1; first-order rate constants for dissociation of the EI complexes are in the range 1-4 x 10-4 s-1. The association rate constants are similar to those measured for D-3-mercapto-2-methylpropanoyl-L-proline, captopril, but the dissociation rate constants are severalfold slower and account for the higher affinity of these inhibitors for the enzyme. The dissociation constant for the EI complex containing N(α)-[(S)-1-carboxy-3-phenylpropyl]L-alanyl-L-proline is pH-dependent, and reaches a minimum at approximately pH 6: K(i) = 4 ± 1 x 10-11 M. The pH dependence is consistent either with a model for which the protonation state of the secondary nitrogen atom in the inhibitor determines binding affinity, or one for which ionizations on the enzyme alone influence affinity for these inhibitors. The affinity of this inhibitor for the zinc-free apoenzyme is 2 x 104 times less than that for the holoenzyme. If considered as a 'collected product' inhibitor, N(α)-[(S)-1-carboxy-3-phenylprolyl]L-alanyl-L-proline appears to derive an additional factor of 375 M in its affinity for the enzyme compared to that of the two products of its hypothetical hydrolysis, a consequence of favorably entropy effects.